Update requirements.txt

notebooks/analysis/requirements.txt

@@ -1,169 +1,148 @@
-## The following requirements were added by pip freeze:
 agct==0.1.0.dev1
 aiofiles==23.2.1
 annotated-types==0.6.0
 anyio==4.3.0
+appdirs==1.4.4
 appnope==0.1.4
-argcomplete==3.3.0
-argh==0.31.2
-argon2-cffi==23.1.0
-argon2-cffi-bindings==21.2.0
-arrow==1.3.0
 asttokens==2.4.1
-async-lru==2.0.4
+async-timeout==4.0.3
 asyncpg==0.29.0
 attrs==23.2.0
-Babel==2.14.0
 beautifulsoup4==4.12.3
+biocommons==0.0.0
 biocommons.seqrepo==0.6.9
 biopython==1.83
+bioservices==1.11.2
 bioutils==0.5.8.post1
-bleach==6.1.0
-boto3==1.34.88
-botocore==1.34.88
+boto3==1.34.69
+botocore==1.34.69
+bs4==0.0.2
 canonicaljson==2.0.0
+cattrs==24.1.2
+cdot==0.2.26
 certifi==2024.2.2
-cffi==1.16.0
 cfgv==3.4.0
 charset-normalizer==3.3.2
 click==8.1.7
+colorama==0.4.6
 coloredlogs==15.0.1
+colorlog==6.8.2
 comm==0.2.2
-configparser==7.0.0
-cool_seq_tool==0.4.0.dev3
-coverage==7.4.4
-dcd_mapping==0.1.3
+configparser==6.0.1
+contourpy==1.3.0
+cool_seq_tool==0.6.0
+coverage==7.6.1
+cycler==0.12.1
+dcd_mapping==0.3.0
 debugpy==1.8.1
 decorator==5.1.1
-defusedxml==0.7.1
 distlib==0.3.8
+easydev==0.13.2
+eutils==0.6.0
 executing==2.0.1
-fastapi==0.110.2
-fastjsonschema==2.19.1
-filelock==3.13.4
-fqdn==1.5.1
+fastapi==0.110.0
+filelock==3.16.1
+fonttools==4.54.1
 fqfa==1.3.1
-ga4gh.vrs==2.0.0a6
-gene-normalizer==0.3.0.dev1
-gffutils==0.13
+ga4gh.vrs==2.0.0a10
+gene-normalizer==0.4.1
+gevent==24.2.1
+greenlet==3.1.1
+grequests==0.7.0
 h11==0.14.0
 hgvs==1.5.4
-httpcore==1.0.5
-httpx==0.27.0
+httpcore==1.0.6
+httpx==0.26.0
 humanfriendly==10.0
-identify==2.5.36
-idna==3.7
+identify==2.6.1
+idna==3.6
+idutils==1.2.1
 importlib_metadata==7.1.0
 iniconfig==2.0.0
-ipykernel==6.29.4
-ipython==8.23.0
-ipywidgets==8.1.2
-isoduration==20.11.0
+intervaltree==3.1.0
+ipykernel==6.29.3
+ipython==8.22.2
+isbnlib==3.10.14
 jedi==0.19.1
-Jinja2==3.1.3
+Jinja2==3.1.5
 jmespath==1.0.1
-json5==0.9.25
-jsonpointer==2.4
-jsonschema==4.21.1
-jsonschema-specifications==2023.12.1
-jupyter==1.0.0
-jupyter-console==6.6.3
-jupyter-events==0.10.0
-jupyter-lsp==2.2.5
 jupyter_client==8.6.1
 jupyter_core==5.7.2
-jupyter_server==2.14.0
-jupyter_server_terminals==0.5.3
-jupyterlab==4.1.6
-jupyterlab_pygments==0.3.0
-jupyterlab_server==2.27.0
-jupyterlab_widgets==3.0.10
-MarkupSafe==2.1.5
-matplotlib-inline==0.1.7
+kiwisolver==1.4.7
+lazy==1.6
+line_profiler==4.1.3
+lxml==5.3.0
+MarkupSafe==3.0.2
+matplotlib==3.9.2
+matplotlib-inline==0.1.6
+mavedb==2024.1.0
 mavehgvs==0.6.1
-mistune==3.0.2
-nbclient==0.10.0
-nbconvert==7.16.3
-nbformat==5.10.4
 nest-asyncio==1.6.0
-nodeenv==1.8.0
-notebook==7.1.3
-notebook_shim==0.2.4
+nodeenv==1.9.1
 numpy==1.26.4
-overrides==7.7.0
 packaging==24.0
-pandas==2.2.2
-pandocfilters==1.5.1
+pandas==1.4.4
 Parsley==1.3
-parso==0.8.4
+parso==0.8.3
 pexpect==4.9.0
+pillow==10.4.0
 platformdirs==4.2.0
+plottable==0.1.5
 pluggy==1.5.0
-polars==0.20.22
-pre-commit==3.7.0
-prometheus_client==0.20.0
+polars==1.8.2
+pre-commit==3.8.0
 prompt-toolkit==3.0.43
 psutil==5.9.8
 psycopg==3.1.18
 psycopg-binary==3.1.18
 psycopg2==2.9.9
 ptyprocess==0.7.0
 pure-eval==0.2.2
-pycparser==2.22
-pydantic==2.7.0
-pydantic_core==2.18.1
-pyfaidx==0.8.1.1
+pydantic==2.9.2
+pydantic_core==2.23.4
 Pygments==2.17.2
-pyliftover==0.4.1
+pyhumps==3.8.0
+pyparsing==3.1.4
 pysam==0.22.0
-pytest==8.1.1
-pytest-asyncio==0.23.6
+pytest==8.3.3
+pytest-asyncio==0.24.0
 pytest-cov==5.0.0
 pytest-mock==3.14.0
 python-dateutil==2.9.0.post0
-python-dotenv==1.0.1
-python-json-logger==2.0.7
+python-dotenv==0.20.0
 pytz==2024.1
 PyYAML==6.0.1
-pyzmq==26.0.2
-qtconsole==5.5.1
-QtPy==2.4.1
-referencing==0.34.0
+pyzmq==25.1.2
 requests==2.31.0
+requests-cache==1.2.1
 requests-mock==1.12.1
-rfc3339-validator==0.1.4
-rfc3986-validator==0.1.1
-rpds-py==0.18.0
-ruff==0.2.0
+ruff==0.5.0
 s3transfer==0.10.1
-Send2Trash==1.8.3
-setuptools==69.5.1
-setuptools-scm==8.1.0
-simplejson==3.19.2
+seaborn==0.13.2
 six==1.16.0
 sniffio==1.3.1
+sortedcontainers==2.4.0
 soupsieve==2.5
-sqlparse==0.5.0
+SQLAlchemy==2.0.35
+sqlparse==0.4.4
 stack-data==0.6.3
-starlette==0.37.2
+starlette==0.36.3
+suds-community==1.2.0
 tabulate==0.9.0
-terminado==0.18.1
-tinycss2==1.2.1
 tornado==6.4
 tqdm==4.66.2
-traitlets==5.14.3
-types-python-dateutil==2.9.0.20240316
-typing_extensions==4.11.0
+traitlets==5.14.2
+typing_extensions==4.10.0
 tzdata==2024.1
-uri-template==1.3.0
+url-normalize==1.4.3
 urllib3==1.26.18
 uvicorn==0.29.0
-virtualenv==20.25.3
+virtualenv==20.26.6
 wags_tails==0.1.3
 wcwidth==0.2.13
-webcolors==1.13
-webencodings==0.5.1
-websocket-client==1.7.0
-widgetsnbextension==4.0.10
+wrapt==1.16.0
+xmltodict==0.14.0
 yoyo-migrations==8.2.0
 zipp==3.18.1
+zope.event==5.0
+zope.interface==7.0.3